Re: [AMBER] sander job crashed

From: Ben Roberts <ben.roberts.geek.nz>
Date: Thu, 7 Jul 2011 20:02:30 -0400

Hi Mustafa,

On 7/7/2011, at 7:37 a.m., MUSTAFA BUGHIO wrote:

> My job is crashed every time i run sander i dont know how can i over come
> this problem.
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> In the VDWAALS i guess there is some prblem. The no of residue in my PDB
> file are 1545. Does this cause any problem in runnig sander?
> BOND = 1465.5323 ANGLE = 5076.3024 DIHED = 14472.5720
> VDWAALS = ************* EEL = -549369.0011 HBOND =
> 0.0000
> 1-4 VDW = 89309.3369 1-4 EEL = 71549.2051 RESTRAINT =
> 0.2644
> EAMBER = *************
>
> Reply plz

What exactly are you trying to run? If you're trying to do MD, it appears as
though you haven't minimised your system first, and you have pairs of atoms that
are too close to each other. Running an energy minimisation before starting MD
is essential.

If this is not your difficulty, please post your mdin file so we can see what it
is you're trying to do.

Regards,
Ben

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Received on Thu Jul 07 2011 - 17:30:03 PDT
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